From September 1, 2020, re-enter to Japan and leaving from Japan are possible.
If you are planning to leave from Japan between 1st of September to 6th of September, you can apply your re-entry permit at the immigration desk in the airport.
If you are planning to re-enter to Japan, you must have PCR-test 72 hours before you leave to Japan
If you are from the country which sill on the list of rejection of travel, you need to stay at a hotel 14 days after you arrive.
This is only for people who already holds re-entry permit and official residence status in Japan, so that NOT for new comer and tourists.
Here is the announcement by the immigration office